fnins-12-00664 September 27, 2018 Time: 15:25 # 1 METHODS published: 25 September 2018 doi: 10.3389/fnins.2018.00664 A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble Edited by: Yu-Guo Yu, Jay S. Coggan1 †, Corrado Calì2 †, Daniel Keller1, Marco Agus3,4, Daniya Boges2, Fudan University, China * * Marwan Abdellah1, Kalpana Kare2, Heikki Lehväslaiho2,5, Stefan Eilemann1, Reviewed by: Renaud Blaise Jolivet6,7, Markus Hadwiger3, Henry Markram1, Felix Schürmann1 and Clare Howarth, Pierre J. Magistretti2 University of Sheffield, United Kingdom 1 Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland, 2 Biological and Environmental Ying Wu, Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, 3 Visual Xi’an Jiaotong University, China Computing Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, 4 CRS4, Center of Research *Correspondence: and Advanced Studies in Sardinia, Visual Computing, Pula, Italy, 5 CSC – IT Center for Science, Espoo, Finland, Jay S. Coggan 6 Département de Physique Nucléaire et Corpusculaire, University of Geneva, Geneva, Switzerland, 7 The European jay.coggan@epfl.ch; Organization for Nuclear Research, Geneva, Switzerland [email protected] Corrado Calì [email protected]; One will not understand the brain without an integrated exploration of structure and [email protected] function, these attributes being two sides of the same coin: together they form the †These authors share first authorship currency of biological computation. Accordingly, biologically realistic models require the re-creation of the architecture of the cellular components in which biochemical reactions Specialty section: This article was submitted to are contained. We describe here a process of reconstructing a functional oligocellular Neuroenergetics, Nutrition and Brain assembly that is responsible for energy supply management in the brain and creating Health, a computational model of the associated biochemical and biophysical processes. The a section of the journal Frontiers in Neuroscience reactions that underwrite thought are both constrained by and take advantage of brain Received: 31 May 2018 morphologies pertaining to neurons, astrocytes and the blood vessels that deliver Accepted: 04 September 2018 oxygen, glucose and other nutrients. Each component of this neuro-glio-vasculature Published: 25 September 2018 ensemble (NGV) carries-out delegated tasks, as the dynamics of this system provide Citation: Coggan JS, Calì C, Keller D, Agus M, for each cell-type its own energy requirements while including mechanisms that allow Boges D, Abdellah M, Kare K, cooperative energy transfers. Our process for recreating the ultrastructure of cellular Lehväslaiho H, Eilemann S, components and modeling the reactions that describe energy flow uses an amalgam of Jolivet RB, Hadwiger M, Markram H, Schürmann F and Magistretti PJ state-of the-art techniques, including digital reconstructions of electron micrographs, (2018) A Process for Digitizing advanced data analysis tools, computational simulations and in silico visualization and Simulating Biologically Realistic Oligocellular Networks Demonstrated software. While we demonstrate this process with the NGV, it is equally well adapted for the Neuro-Glio-Vascular to any cellular system for integrating multimodal cellular data in a coherent framework. Ensemble. Front. Neurosci. 12:664. doi: 10.3389/fnins.2018.00664 Keywords: electron microscopy, 3D reconstruction, simulation, NGV, energy metabolism, in silico visualization Frontiers in Neuroscience | www.frontiersin.org 1 September 2018 | Volume 12 | Article 664 fnins-12-00664 September 27, 2018 Time: 15:25 # 2 Coggan et al. Building Biorealistic in silico Cellular Simulations INTRODUCTION The limitations of geometrically and spatially simplistic models entreats a better approach: thinking “outside-the-box,” so to Overview speak, requires thinking about what’s happening “inside-the- We present a snapshot of progress in the development of a box”; one must consider the complexity of the internal cellular universal process for the creation of morphologically accurate complement of organelles and macromolecular complexes, as digital reconstructions of a functional assembly of cells for the well as local “virtual” micro-environments created by, for purpose of conducting biologically realistic computer simulations example, restricted diffusion, lipid-water interfaces and non- and in silico experiments. Our goal is to explore and understand uniform protein expression (e.g., Berridge, 2006; Shillcock, cooperative biochemical and biophysical functions of networks 2008). of several cells (oligocellular networks). Specifically, we focus on Perhaps the most prevalent method for discovering the micro- the re-creation of the neuro-glio-vasculature (NGV) ensemble architecture of life has been electron microscopy (EM). This and our multi-scale energetics modeling program. Although we technique has a storied past in the annals of cell biology apply this system to our particular interest in brain energy from the first pictures of eukaryotic cells (Porter et al., 1945) metabolism, our procedure can be applied to any oligocellular to the pioneering studies on organelles such as mitochondria grouping from any tissue or species. This innovative procedure (Palade, 1952), discernment of macromolecular processes such uses state-of-the-art techniques and software developed primarily as muscle contraction filaments (Huxley, 1957), and proof by a collaborative alliance between the Blue Brain Project for the neuron doctrine (Palade and Porter, 1954). Of great (BBP) of the École Polytechnique Fédérale de Lausanne (EPFL), importance to neuroscience have been the demonstration of in Switzerland, and the King Abdullah University of Science pre-synaptic vesicles (De Robertis and Bennett, 1955), the first and Technology (KAUST), in Saudi Arabia, with the aim entire nervous system (White et al., 1986) and the possible of facilitating the advancement neuroscience with in silico structural correlates of learning (Trachtenberg et al., 2002; methods. The workflow, designed in 4 stages, addresses previous de Vivo et al., 2017). No less important to neuroscience inadequacies in resolution and accuracy of imaging, seeks to are the astrocytes (Vaughn and Pease, 1967; Bushong et al., automate many labor-intensive steps, implements multi-scale 2004) and the particulars of their subcellular milieu such as modeling and uses advances in in silico imaging and large- the localization of the glycogen macromolecular complexes scale visualization techniques, including virtual reality (VR), as that are so critical to the energy supply to brain tissue (Oe research tools. et al., 2016) – this latter type of data requiring advanced three-dimensional (3D) EM techniques (Calì et al., 2016, 2017; Calì, 2017). The importance of the 3D arrangement Cytoscale in silico Neuroscience of astrocytic processes has been evident since the 1960s Simulation-based research, often referred to as the in silico when early observations of astrocytes from serial section EM method, is establishing itself as an indispensable tool to bridge appeared (Wolff, 1965; Stensaas and Stensaas, 1967; Poritsky, physical and temporal scales, enhance insights and accelerate 1969). progress in more and more scientific disciplines. In biology, it By taking the detailed 3D environment of biological systems has long been recognized that mathematical modeling would be into consideration in addition to kinetic properties, a spatial- required to complement experimental efforts to understand basic temporal simulation approach becomes superior for revealing principles of life’s complexity, ranging from cellular phenomena and understanding fundamental principles. The efficacy of this (Hodgkin and Huxley, 1952; Del Castillo and Katz, 1954; Joyner synergism has been demonstrated at various scales. Fundamental et al., 1978; Bartol et al., 1991; Stephanova and Bostock, 1995; functions that could not have been measured, observed or Tsodyks and Markram, 1997; Nadkarni and Jung, 2007; Coggan predicted based on experiments alone have emerged from this et al., 2010; Xylouris and Wittum, 2015) to network behavior (e.g., kind of simulation from the sub-cellular level toward one end Eliasmith et al., 2002; Izhikevich, 2004; Migliore et al., 2006), just of the domain scale (e.g., Coggan et al., 2005; Keller et al., 2008; to name a few. This realization has engendered the creation of Bartol et al., 2015), to the mammalian cortical circuit level toward multiple simulation environments to address this need (Bartol the other end (e.g., Markram et al., 2015; Reimann et al., 2017), et al., 1991; Hines and Carnevale, 1997; Bower and Beeman, while the most comprehensive effort to create an anatomically 1998; Tomita et al., 1999; Schaff et al., 2000; Eppler et al., 2008). and physiologically realistic simulation of an entire organism, Our simulation niche, involving a few interacting cells, is often demonstrated in the roundworm Caenorhabditis elegans by the given the cytoscale designation, an intermediate level between OpenWorm project1, has witnessed the first re-creations of molecular and higher-order network models. animal behaviors with a predictive modeling approach (Szigeti There are many approaches to modeling in biology depending et al., 2014). In these and other cases,